In response to this threat, Jackson chose to go on the offensive, attacking Pope's vanguard under Banks, before the entire Army of Virginia could be brought to bear on his position at Gordonsville.[5] After defeating Banks, he then hoped to move on Culpeper Court House, 26 miles (42 km) north of Gordonsville and the focal point of the Union arc about Northern Virginia, to keep Pope's army from uniting. This would allow Jackson to fight and hopefully defeat each of the Union Corps separately, as he had done during the Valley Campaign. Accordingly, Jackson set out on August 7 for Culpeper.[6] The cavalry under Brig. Gen. Beverly Robertson was sent ahead to dispatch the Federal cavalry guarding the fords of the Rapidan River and occupying Madison Court House, threatening the Confederates left flank as they marched northward. This task was easily accomplished by Robertson on August 8.[7]

Jackson's march on Culpeper Court House was hindered by the severe heat wave over Virginia at the beginning of August, as well as by his characteristic secrecy about his plan, which caused confusion among his divisional commanders as to the exact route of advance. As such, the head of his column had only progressed 8 miles (13 km) by the evening of August 8. The Federal Cavalry, though easily dispatched by Robertson, quickly returned to Pope and alerted him of the Confederate advance. In response, Pope ordered Sigel to Culpeper Court House to reinforce Banks, and Banks was ordered to maintain a defensive line on a ridge above Cedar Run, 7 miles (11 km) south of Culpeper Court House.[8]

On the morning of August 9, Jackson's army crossed the Rapidan River into Culpeper County, led by Maj. Gen. Richard S. Ewell's division, followed by Brig. Gen. Charles S. Winder's division, with Maj. Gen. A.P. Hill's division in the rear. Just before noon, Brig. Gen. Jubal Early's brigade, the vanguard of Ewell's division, came upon Federal cavalry and artillery occupying the ridge above Cedar Run, just to the north-west of Cedar Mountain. Early brought up his guns and an artillery duel began between the opposing forces as Early's infantry formed a line on the eastern side of the Culpeper-Orange Turnpike (present day U.S. Route 15) on the high ground on the opposite bank of Cedar Run.[9] As the rest of Ewell's division arrived they formed on Early's right, anchored against the northern slope of the mountain and deployed their six guns on its ridge. Winder's division formed to Early's left, on the west side of the Turnpike, with Brig. Gen. William Taliaferro's brigade closest to Early, and Col. Thomas S. Garnett's on the far Confederate left in a wheat field at the edge of a woods. Winder's artillery filled a gap on the road between the two divisions. The Stonewall Brigade, led by Col. Charles R. Ronald, was brought up in support behind the guns. A.P Hill's division, still marching up the Turnpike, was ordered to stand in reserve on the Confederate left.[10]

The Federals formed a line on a ridge above Cedar Run, with Brig. Gen. Samuel W. Crawford's brigade forming the Union right in a field across from Garnett and Brig. Gen. Christopher C. Augur's division on the Union left to the east of the Turnpike. Brig. Gen. John W. Geary's brigade was anchored on the Turnpike opposing Taliaferro, while Brig. Gen Henry Prince's brigade formed the far left opposite Ewell. Brig. Gen. George S. Greene's understrength brigade (only two regiments) was kept in reserve in the rear.[11]

Cedar Mountain battlefield, facing south from the approximate southwestern corner of the wheat field

A little before 5:00 p.m. as the artillery fight began to wane, Confederate Brig. Gen. Charles S. Winder fell mortally wounded. He had been ill that day and was taken onto the field in an ambulance wagon. While attempting to direct his troops, he was struck by a shell fragment. Winder's left arm and side were torn to pieces, and he died a few hours later. As a result, command of the division devolved on William Taliaferro, who was completely ignorant of Jackson's battle plan. Dispositions on his part of the field were still incomplete; Garnett's brigade was isolated from the main Confederate line, with its flank dangerously exposed to the woods. The Stonewall Brigade was to have come up to support them, but remained a half mile distant behind the artillery.[12] Before leadership could properly be restored to the division the Union attack began. Geary and Prince were sent against the Confederate right. The Federal advance was swift and threatened to break the Confederate line, prompting Early to come galloping to the front from Cedar Mountain where he was directing troop dispositions. Early's stabilizing presence and the raking fire of the Confederate guns halted the Union advance on the Confederate right.[11] On the left Crawford attacked Winder's division, sending one brigade directly at the Confederate line and another brigade through the woods on a flanking movement. The Federals came from the woods directly into the flank of the 1st Virginia Infantry, who under the pressure from attack on two fronts broke for the rear. The Federals pushed on, not waiting to reform their lines, rolling through the outflanked 42nd Virginia until they found themselves in Taliaferro's and the artillery's rear. The Stonewall Brigade came up and was swept aside by Crawford's troops before it had a chance to react. Jackson ordered the batteries withdrawn before they were captured, but Taliaferro and Early's left were hit hard by the Union advance and threatened to break.[13]

At this dire point, Gen. Jackson rode to that part of the field to rally the men and came upon his old brigade finally being brought up to reinforce the line. Intending to inspire the troops there, he attempted to brandish his sword; however, due to the infrequency with which he drew it, it had rusted in its scabbard and he was unable to dislodge it. Undaunted, he unbuckled the sword from his belt and waved it, scabbard and all, over his head. He then grabbed a battle flag from a retreating standard bearer and yelled at his men to rally around him.[14] The Stonewall Brigade, heartened by their commander, launched into the Union troops and drove them back. By this point, Banks's men were becoming tired and disorganized, with their ammunition nearly gone. Without any support, his men had been unable to follow up on their initial success. In their zeal, the Stonewall Brigade pursued the Federals as they fell back, but soon found themselves beyond the Confederate line and without support. The Federals reformed and attacked, driving the 4th and 27th Virginia back. But the actions of the Stonewall Brigade gave the Confederate line time to reform and A.P Hill's troops to come up and fill the gaps from Winder's broken regiments.[15] Jackson ordered Hill and Ewell to advance. He encountered Brig. Gen. Lawrence O'Bryan Branch (a career politician) making a lengthy speech to his troops, and urged him to press forward. The Union right immediately collapsed. Ewell, having difficulty silencing his guns, was delayed, but the Union left began to waver at the sight of Crawford's retreat and were finally broken by a charge down Cedar Mountain by Brig. Gen. Isaac R. Trimble's brigade.[16]

Despite bringing up Greene's reserve brigade in support, by 7:45 p.m. the Union line was in full retreat. In a last-ditch effort to help cover his infantry's retreat, Banks sent two squadrons of cavalry at the Confederate line. They were met with a devastating volley from the Confederate infantry posted behind a fence on the road, allowing only 71 of 174 to escape.[15] The Confederate infantry and Brig. Gen William E. Jones's 7th Virginia Cavalry hotly pursued the retreating Federals, nearly capturing Banks and Pope, who were at their headquarters a mile behind the Federal line.[17] After a mile-and-a-half of pursuit, Jackson grew weary as darkness set in, as he was unsure of the location of the rest of Pope's army. Finally, several Union infantrymen captured by the 7th Virginia informed the Confederates that Pope was bringing Sigel forward to reinforce Banks. Accordingly, Jackson called off the pursuit and by around 10 p.m the fighting had ceased. By this point, Brig. Gen. James Ricketts's division of McDowell's corps was arriving, which effectively covered Banks's retreat.[18]

Losses were high in the battle: Union casualties of 2,353 (314 killed, 1,445 wounded, 594 missing), Confederate 1,338 (231 killed, 1,107 wounded).[1] Crawford's brigade had lost over 50% of its total strength, including most of its officers. Prince's and Geary's brigades suffered 30–40% casualty rates. Both generals were wounded, and Prince was also captured.[19] Confederate Brig. Gen. Charles S. Winder was mortally wounded by a shell.

For two days, Jackson maintained his position south of Cedar Run on the western slope of the mountain, waiting for a Federal attack that did not come. Finally, receiving news that all of Pope's army had arrived at Culpeper Court House, on August 12, Jackson fell back on Gordonsville to a more defensive position behind the Rapidan River.[20]

Weather and poor communication with his divisional commanders had robbed Jackson of the initiative in the fight. Still expecting to face the same cautious opponent from the Valley, he was taken by surprise and very nearly driven from the field. Excellent commanding by the Confederates at the crucial moment of the battle and the fortuitous arrival of Hill staved off defeat, eventually allowing their numerical superiority to drive the Federals from the field. For his part, Banks, having been soundly defeated by Jackson in the Valley, was anxious to make up for previous losses. Rather than fighting a defensive battle from a strong position because he was outnumbered 2 to 1, giving time for the rest of Pope's army to arrive, he decided to take the initiative and attack Jackson before he could fully form his lines. The bold move very nearly paid off, but in the end he was again defeated by his old foe.[21]

With Jackson on the loose, wreaking havoc against Union forces, General-in-Chief Henry W. Halleck became apprehensive and called off Pope's advance on Gordonsville, thereby giving Lee the initiative in the Northern Virginia Campaign. The battle effectively shifted fighting in Virginia from the Virginia Peninsula into northern Virginia.[17]

The Civil War Trust has preserved 164 acres of the Cedar Mountain battlefield to September 2015.[22]

Most of the already preserved land sits near the intersection of Virginia State Routes 15 and 657 (the latter of which is known as General Winder Road). It includes the area where Crittenden Gate once stood, along with the wheat field in which some of the bloodiest fighting of the battle took place. The Trust preserved a 152-acre plot of land there in 1998, added two more to that total twelve years later and ten more by 2013. A local organization known as the Friends of Cedar Mountain Battlefield proved instrumental to implementing these preservation efforts.[23]

The ten acres saved in 2012 are close to Crittenden Gate site and included the area of the battlefield where General Winder was mortally wounded, along with the locations of Jackson’s command post and his desperate effort to rally Confederate troops at the climax of the battle.[24]